The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
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DOI：
10.1021/acs.jctc.7b00125
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发表时间：
2017-06-01
影响因子：
5.5
通讯作者：
Gray, Jeffrey J.
中科院分区：
文献类型：
--
作者：
Alford, Rebecca F.;Leaver-Fay, Andrew;Gray, Jeffrey J.
在过去的十年中，Rosetta生物分子建模套件为各种生物学问题和工程挑战提供了信息，从低分辨率结构数据的解释到纳米材料，蛋白质治疗和疫苗的设计。Rosetta成功的核心是能量函数：一个由小分子和X射线晶体结构数据参数化的模型，用于近似与每个生物分子构象相关的能量。本文描述了最新Rosetta能量函数（称为Rosetta能量函数2015（REF 15））的数学模型和物理概念。应用这些概念，我们解释了如何使用Rosetta能量来识别和分析生物分子模型的特征。最后，我们讨论了能量函数的最新进展，从可溶性蛋白质扩展到膜蛋白，含有非典型氨基酸的肽，小分子，碳水化合物，核酸和其他大分子。
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15). Applying these concepts, we explain how to use Rosetta energies to identify and analyze the features of biomolecular models. Finally, we discuss the latest advances in the energy function that extend its capabilities from soluble proteins to also include membrane proteins, peptides containing noncanonical amino acids, small molecules, carbohydrates, nucleic acids, and other macromolecules.